ITPR2 p.Phe1958=
c.5874T>C · rs139925842 · VCV3033955
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0549%, nfe)
Conditions
1
ITPR2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.57 | GERP -5, phastCons 0.002 |
| Overall | ||
| CADD | 5.531 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0549%
European (non-Finnish) · 648/1,180,032 alleles
Filtering AF
0.0513%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.05%
Overall
0.0445%
719/1,614,206 alleles · ultra-rare
exomes 656/1,461,878 · genomes 63/152,328 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0549% | 1,821 |
| Admixed American | 0.05% | 2,001 |
| Middle Eastern | 0.0495% | 2,021 |
| Remaining individualsnot grpmax-eligible | 0.0432% | 2,315 |
| African / African-American | 0.00799% | 12,510 |
| South Asian | 0.00439% | 22,771 |
| Finnishnot grpmax-eligible | 0.00156% | 64,030 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- ITPR2
- Protein
- p.Phe1958=
- Coding
- c.5874T>C
- MANE Select
- NM_002223
- dbSNP
- rs139925842
- Type
- single nucleotide variant
- Location
- chr12:26483836 (GRCh38)
- Gene constraint
- LOEUF 0.724 · pLI <0.01 (gnomAD)
Disease context
ITPR2-related disorder
Similar variants
- ITPR2 c.279+6G>C Benign same condition
- ITPR2 c.3122+4T>C Likely benign same condition
- ITPR2 c.3552+3C>T Likely benign same condition
- ITPR2 c.4381-8C>T Likely benign same condition
- ITPR2 p.Ala2112= Likely benign same condition
- ITPR2 p.Ala898= Benign same condition
- ITPR2 p.Asp2103= Likely benign same condition
- ITPR2 p.Glu815= Likely benign same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/itpr2-p-phe1958 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown